[gmx-users] converting L to D amino acid in the CHARMM force field in GROMACS where to alter dihedral

Hello List I want to change an ASP to a D-ASP. I think it should be possible by simply changing 2 improper values around the chiral carbon to their opposite sign. Instead of making a brand new residue, I thought I would take the topology of an ASP generated by pdb2gmx, and simply change values man

Re: [gmx-users] converting L to D amino acid in the CHARMM force field in GROMACS where to alter dihedral

Hi Maria, The CHARMM force field is an all-atom one. That means it does not require improper dihedrals to maintain chirality. If you have a D-ASP in your structure file, you can rename it to ASP and just run pdb2gmx. Mind not to regenerate hydrogens in that case, or make sure to modify the hydroge

[gmx-users] Regarding the construction of Dynamics cross correlation map from covar.dat(from g_covar)

Hello users, Although there was already much discussion had been done on the procedure to construct DCCM map from covar.dat(i.e. output from g_covar) but still I am not clear with the step wise procedure to calculate the correlation matrix from covarience matrix(covar.dat). 1) It is stated in the

Re: [gmx-users] converting L to D amino acid in the CHARMM force field in GROMACS where to alter dihedral

Hi Appreciate the quick help I am sorry, this is not an improper, but a proper dihedral that holds the chirality in place. Then the solution suggested by Meli would not work? I do not have a D-ASP. I in fact have an L-ASP which i want to convert to D. So the question is simply how to set the prop

Re: [gmx-users] converting L to D amino acid in the CHARMM force field in GROMACS where to alter dihedral

Hi Maria, The general solution is to copy the entry in the .rtp file, modify the dihedrals involved, and rename the entry to match the name used in the coordinate (pdb) file. You may also need to copy the entries in the .hdb file, as well as the .tdb files if it is a terminal residue. Hope it hel

[gmx-users] Citation for NICS

Hello everyone, is this citation proper for citing NICS? I.I. Rabi, J.R. Zacharias, S. Millman, P. Kusch (1938). "A New Method of Measuring Nuclear Magnetic Moment". *Physical Review * *53*: 318. doi

[gmx-users] units for atomic coordinates in traj.xtc? nm?

A very quick question. Can someone confirm that atomic coordinates are stored as in the traj.xtc file in units of nm (as opposed to Angstroms)? I am trying to figure out whether or not in the g_msd program reads in nm or Angstroms. The standard output of the xy graph is nm2 and ps. I can'

Re: [gmx-users] units for atomic coordinates in traj.xtc? nm?

Jennifer Williams wrote: A very quick question. Can someone confirm that atomic coordinates are stored as in the traj.xtc file in units of nm (as opposed to Angstroms)? I am trying to figure out whether or not in the g_msd program reads in nm or Angstroms. The standard output of the xy gra

Antw: [gmx-users] Citation for NICS

Hello, Why do you ask this ? >>> Sergio Manzetti 25.03.11 13.09 Uhr >>> Hello everyone, is this citation proper for citing NICS? I.I. Rabi, J.R. Zacharias, S. Millman, P. Kusch (1938). "A New Method of Measuring Nuclear Magnetic Moment". Physical Review 53: 318. doi:10.1103/PhysRev.53.318.

Re: [gmx-users] Citation for NICS

Beacuse I want to cite NICS. On Fri, Mar 25, 2011 at 8:56 PM, Emanuel Peter < emanuel.pe...@chemie.uni-regensburg.de> wrote: > Hello, > > Why do you ask this ? > > > > >>> Sergio Manzetti 25.03.11 13.09 Uhr >>> > > Hello everyone, is this citation proper for citing NICS? > > I.I. Rabi, J.R. Zacha

Re: [gmx-users] Citation for NICS

Sergio Manzetti wrote: Beacuse I want to cite NICS. Clearly. But posing a question about experimental NMR techniques to the Gromacs software list is probably not the most efficient approach to getting an answer. A quick Google search turns up numerous recent reviews about NICS. Doubtles

[gmx-users] Carbohydrate simulation: problem with the terminal atoms

Hi everyone, I am using g53a6 force filed for the simulation of cellulose. However it seems that parametrization works only for the sugar blocked linked together and no terminal atoms for terminal residues are defined there (I mean the start and end atom, H and O atom at the beginning linked to

Re: [gmx-users] Carbohydrate simulation: problem with the terminal atoms

I am not sure if you have looked through this paper, but it gives the parameters for sugars. A new GROMOS force field for hexopyranose-based carbohydrates by RD Lins, 2005 A biomolecular force field based on the free enthalpy of hydration and solvation: The GROMOS force?field parameter sets

Re: [gmx-users] converting L to D amino acid in the CHARMM force field in GROMACS where to alter dihedral

Yes, that would be the correct way to do this. I was hoping to take a shorter route, and just modifying a couple of dihedrals in the topology files output by pdb2gmx without having to make a new residue. Is that not possible at all ? On Fri, Mar 25, 2011 at 12:24 PM, Tsjerk Wassenaar wrote: > H

[gmx-users] flexible spc water model

Hello, I am want to use flexible spc water model for my simulation. I define=-DFLEX_SPC in my mdp and mentioned #include "spc.itp" in my .top file. Does it correct? I am using gromacs 4.0.7 version. Thanks Nilesh dipcorr.pdf Description: Adobe PDF document -- gmx-users mailing listg

Re: [gmx-users] flexible spc water model

Nilesh Dhumal wrote: Hello, I am want to use flexible spc water model for my simulation. Might I inquire as to why? SPC was parameterized to be rigid, and as has been stated numerous times across the list, flexible water should not be used. I define=-DFLEX_SPC in my mdp and mentioned

[gmx-users] g_cluster segmentation fault

Dear All, When running g_cluster on a file generated with g_mdmat I receive a segmentation fault. I have tried different versions of Gromacs (4.0.5 and 4.5.3) on different workstations with both large and small matrices - all without success. I am calling g_cluster with: g_cluster -dm dmat_

Re: [gmx-users] no output dgdl file

Thank you Justin and Emanuel for helpful remarks. I am a little confused what is the proper detailed procedure to perform FE using TI and BAR when decoupling nonboded terms separately. I write down my understanding and would appreciate your comments. Summary: TI: One needs to vary init_lambda (=n

Re: [gmx-users] no output dgdl file

> 1- I am wondering for each interval say > > Interval 2: > init_lambda = 0.05 > foreign_lambda = 0 0.1 > > how this foreign_lambda 0 is related to the init_lambda = 0 from interval 1 > and the same for foreign_lambda = 0.1 in interval 2 and init_lambda = 0.1 in > interval 3? Is there a physical me

Re: [gmx-users] no output dgdl file

> I am a bit confused on the g_bar part, when it says -f expects multiple > dhdl files. Do we need to run still multiple independent simulations > using different foreign_lambda values? I do not see why we should run > independent simulations, if we use for couple-lambda0 and couple-lambda1 > vdw-q

[gmx-users] Automated RMSD Calculations

Hi All, I would like to calculate RMSDs of a large number of small molecule conformations against a reference conformation, is there a simple software program or method that can be used to perform such calculations? Thanks in advance, Nancy -- gmx-users mailing listgmx-users@gromacs.org http

Re: [gmx-users] Automated RMSD Calculations

Nancy wrote: Hi All, I would like to calculate RMSDs of a large number of small molecule conformations against a reference conformation, is there a simple software program or method that can be used to perform such calculations? This can easily be scripted: http://www.gromacs.org/Document

Re: [gmx-users] Automated RMSD Calculations

Thanks alot for the info. Nancy On Fri, Mar 25, 2011 at 6:22 PM, Justin A. Lemkul wrote: > > > Nancy wrote: > >> Hi All, >> >> I would like to calculate RMSDs of a large number of small molecule >> conformations against a reference conformation, is there a simple software >> program or method t

Re: [gmx-users] converting L to D amino acid in the CHARMM force field in GROMACS where to alter dihedral

On 26/03/2011 2:27 AM, maria goranovic wrote: Yes, that would be the correct way to do this. I was hoping to take a shorter route, and just modifying a couple of dihedrals in the topology files output by pdb2gmx without having to make a new residue. Is that not possible at all ? Unlike (say)

Re: [gmx-users] g_cluster segmentation fault

On 26/03/11, Craig Kitchen wrote: > Dear All, > > When running g_cluster on a file generated with g_mdmat I receive a > segmentation fault. I have tried different versions of Gromacs (4.0.5 and > 4.5.3) on different workstations with both large and small matrices - all > without success. >